Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/MultiframeDicomWriter.cpp @ 66:2e3d22667409
fix
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 25 Nov 2016 20:52:54 +0100 |
parents | 7a3853d51c45 |
children | ff0ef01c332c |
rev | line source |
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0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU Affero General Public License | |
8 * as published by the Free Software Foundation, either version 3 of | |
9 * the License, or (at your option) any later version. | |
10 * | |
11 * This program is distributed in the hope that it will be useful, but | |
12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
14 * Affero General Public License for more details. | |
15 * | |
16 * You should have received a copy of the GNU Affero General Public License | |
17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
18 **/ | |
19 | |
20 | |
16
7a88c614be04
preparing for precompiled headers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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21 #include "../PrecompiledHeadersWSI.h" |
0 | 22 #include "MultiframeDicomWriter.h" |
23 | |
59
7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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24 #include "../../Resources/Orthanc/Core/OrthancException.h" |
7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
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25 #include "../../Resources/Orthanc/Core/Logging.h" |
0 | 26 #include "../DicomToolbox.h" |
27 | |
28 #include <dcmtk/dcmdata/dcuid.h> | |
29 #include <dcmtk/dcmdata/dcdeftag.h> | |
30 #include <dcmtk/dcmdata/dcostrmb.h> | |
31 #include <dcmtk/dcmdata/dcpxitem.h> | |
32 #include <dcmtk/dcmdata/dcpixel.h> | |
33 #include <dcmtk/dcmdata/dcvrat.h> | |
34 | |
35 #include <boost/lexical_cast.hpp> | |
36 | |
14 | 37 #if DCMTK_VERSION_NUMBER <= 360 |
38 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax | |
39 #endif | |
40 | |
41 | |
0 | 42 namespace OrthancWSI |
43 { | |
44 static void SaveDicomToMemory(std::string& target, | |
45 DcmFileFormat& dicom, | |
46 E_TransferSyntax transferSyntax) | |
47 { | |
48 dicom.validateMetaInfo(transferSyntax); | |
49 dicom.removeInvalidGroups(); | |
50 | |
51 E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; | |
52 | |
53 // Create a memory buffer with the proper size | |
54 { | |
55 const uint32_t estimatedSize = dicom.calcElementLength(transferSyntax, encodingType); // (*) | |
56 target.resize(estimatedSize); | |
57 } | |
58 | |
59 DcmOutputBufferStream ob(&target[0], target.size()); | |
60 | |
61 // Fill the memory buffer with the meta-header and the dataset | |
62 dicom.transferInit(); | |
63 OFCondition c = dicom.write(ob, transferSyntax, encodingType, NULL, | |
64 /*opt_groupLength*/ EGL_recalcGL, | |
65 /*opt_paddingType*/ EPD_withoutPadding); | |
66 dicom.transferEnd(); | |
67 | |
68 if (!c.good()) | |
69 { | |
70 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
71 } | |
72 | |
73 // The DICOM file is successfully written, truncate the target | |
74 // buffer if its size was overestimated by (*) | |
75 ob.flush(); | |
76 | |
77 size_t effectiveSize = static_cast<size_t>(ob.tell()); | |
78 if (effectiveSize < target.size()) | |
79 { | |
80 target.resize(effectiveSize); | |
81 } | |
82 } | |
83 | |
84 | |
85 void MultiframeDicomWriter::ResetImage() | |
86 { | |
87 perFrameFunctionalGroups_.reset(new DcmSequenceOfItems(DCM_PerFrameFunctionalGroupsSequence)); | |
88 | |
89 if (compression_ != ImageCompression_None) | |
90 { | |
91 compressedPixelSequence_.reset(new DcmPixelSequence(DcmTag(DCM_PixelData, EVR_OB))); | |
92 | |
93 offsetTable_ = new DcmPixelItem(DCM_Item, EVR_OB); | |
94 compressedPixelSequence_->insert(offsetTable_); | |
95 offsetList_.reset(new DcmOffsetList); | |
96 } | |
97 | |
98 writtenSize_ = 0; | |
99 framesCount_ = 0; | |
100 } | |
101 | |
102 | |
103 void MultiframeDicomWriter::InjectUncompressedPixelData(DcmFileFormat& dicom) | |
104 { | |
105 static const size_t GIGABYTE = 1024 * 1024 * 1024; | |
106 | |
107 std::string pixelData; | |
108 uncompressedPixelData_.Flatten(pixelData); | |
109 | |
110 // Prevent the creation of too large DICOM files | |
111 // (uncompressed DICOM files are limited to 2GB) | |
112 if (pixelData.size() > GIGABYTE) | |
113 { | |
114 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); | |
115 } | |
116 | |
117 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(DCM_PixelData)); | |
118 | |
119 uint8_t* target = NULL; | |
120 if (!pixels->createUint8Array(pixelData.size(), target).good()) | |
121 { | |
122 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
123 } | |
124 | |
125 if (pixelData.size() > 0) | |
126 { | |
127 if (target == NULL) | |
128 { | |
129 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
130 } | |
131 | |
132 // TODO Avoid this memcpy() | |
133 memcpy(target, pixelData.c_str(), pixelData.size()); | |
134 } | |
135 | |
136 if (!dicom.getDataset()->insert(pixels.release(), false, false).good()) | |
137 { | |
138 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
139 } | |
140 } | |
141 | |
142 | |
143 MultiframeDicomWriter::MultiframeDicomWriter(const DcmDataset& dataset, | |
144 ImageCompression compression, | |
145 Orthanc::PixelFormat pixelFormat, | |
146 unsigned int width, | |
147 unsigned int height, | |
148 unsigned int tileWidth, | |
149 unsigned int tileHeight) : | |
150 compression_(compression), | |
151 width_(width), | |
152 height_(height) | |
153 { | |
154 switch (compression) | |
155 { | |
156 case ImageCompression_None: | |
157 transferSyntax_ = EXS_LittleEndianImplicit; | |
158 break; | |
159 | |
160 case ImageCompression_Jpeg: | |
161 // Default transfer syntax for lossy JPEG 8bit compression | |
14 | 162 transferSyntax_ = EXS_JPEGProcess1; |
0 | 163 break; |
164 | |
165 case ImageCompression_Jpeg2000: | |
166 // JPEG2000 compression (lossless only) | |
167 transferSyntax_ = EXS_JPEG2000LosslessOnly; | |
168 break; | |
169 | |
170 default: | |
171 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
172 } | |
173 | |
174 if (!sharedTags_.copyFrom(dataset).good()) | |
175 { | |
176 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
177 } | |
178 | |
179 // We only take care of grayscale or RGB images in 8bpp | |
180 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixColumns, width); | |
181 DicomToolbox::SetUint32Tag(sharedTags_, DCM_TotalPixelMatrixRows, height); | |
182 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PlanarConfiguration, 0); // Interleaved RGB values | |
183 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Columns, tileWidth); | |
184 DicomToolbox::SetUint16Tag(sharedTags_, DCM_Rows, tileHeight); | |
185 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsAllocated, 8); | |
186 DicomToolbox::SetUint16Tag(sharedTags_, DCM_BitsStored, 8); | |
187 DicomToolbox::SetUint16Tag(sharedTags_, DCM_HighBit, 7); | |
188 DicomToolbox::SetUint16Tag(sharedTags_, DCM_PixelRepresentation, 0); // Unsigned values | |
189 | |
190 switch (pixelFormat) | |
191 { | |
192 case Orthanc::PixelFormat_RGB24: | |
193 uncompressedFrameSize_ = 3 * tileWidth * tileHeight; | |
194 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 3); | |
195 | |
196 if (compression_ == ImageCompression_Jpeg) | |
197 { | |
198 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "YBR_FULL_422"); | |
199 } | |
200 else | |
201 { | |
202 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "RGB"); | |
203 } | |
204 | |
205 break; | |
206 | |
207 case Orthanc::PixelFormat_Grayscale8: | |
208 uncompressedFrameSize_ = tileWidth * tileHeight; | |
209 DicomToolbox::SetUint16Tag(sharedTags_, DCM_SamplesPerPixel, 1); | |
210 DicomToolbox::SetStringTag(sharedTags_, DCM_PhotometricInterpretation, "MONOCHROME2"); | |
211 break; | |
212 | |
213 default: | |
214 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
215 } | |
216 | |
217 ResetImage(); | |
218 } | |
219 | |
220 | |
221 void MultiframeDicomWriter::AddFrame(const std::string& frame, | |
222 DcmItem* functionalGroup) // This takes the ownership | |
223 { | |
224 // Free the functional group on error | |
225 std::auto_ptr<DcmItem> functionalGroupRaii(functionalGroup); | |
226 | |
227 if (compression_ == ImageCompression_None) | |
228 { | |
229 if (frame.size() != uncompressedFrameSize_) | |
230 { | |
231 LOG(ERROR) << "An uncompressed frame has not the proper size: " | |
232 << frame.size() << " instead of " << uncompressedFrameSize_; | |
233 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
234 } | |
235 | |
236 uncompressedPixelData_.AddChunk(frame); | |
237 } | |
238 else | |
239 { | |
240 uint8_t* bytes = const_cast<uint8_t*>(reinterpret_cast<const uint8_t*>(frame.c_str())); | |
241 | |
242 compressedPixelSequence_->storeCompressedFrame(*offsetList_, bytes, frame.size(), | |
243 0 /* unlimited fragment size */); | |
244 } | |
245 | |
246 if (functionalGroup != NULL) | |
247 { | |
248 perFrameFunctionalGroups_->insert(functionalGroupRaii.release()); | |
249 } | |
250 else | |
251 { | |
252 perFrameFunctionalGroups_->insert(new DcmItem); | |
253 } | |
254 | |
255 writtenSize_ += frame.size(); | |
256 framesCount_ += 1; | |
257 } | |
258 | |
259 | |
260 void MultiframeDicomWriter::Flush(std::string& target, | |
261 unsigned int instanceNumber) | |
262 { | |
263 if (instanceNumber <= 0) | |
264 { | |
265 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
266 } | |
267 | |
268 std::string tmp = boost::lexical_cast<std::string>(instanceNumber); | |
269 | |
270 std::auto_ptr<DcmFileFormat> dicom(new DcmFileFormat); | |
271 | |
272 char uid[100]; | |
273 dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); | |
274 | |
275 if (!dicom->getDataset()->copyFrom(sharedTags_).good() || | |
276 !dicom->getDataset()->insert(perFrameFunctionalGroups_.release(), false, false).good() || | |
277 !dicom->getDataset()->putAndInsertString(DCM_SOPInstanceUID, uid).good() || | |
278 !dicom->getDataset()->putAndInsertString(DCM_InstanceNumber, tmp.c_str()).good()) | |
279 { | |
280 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
281 } | |
282 | |
283 DicomToolbox::SetStringTag(*dicom->getDataset(), DCM_NumberOfFrames, boost::lexical_cast<std::string>(framesCount_)); | |
284 | |
285 switch (compression_) | |
286 { | |
287 case ImageCompression_None: | |
288 InjectUncompressedPixelData(*dicom); | |
289 break; | |
290 | |
291 case ImageCompression_Jpeg: | |
292 case ImageCompression_Jpeg2000: | |
293 offsetTable_->createOffsetTable(*offsetList_); | |
294 dicom->getDataset()->insert(compressedPixelSequence_.release()); | |
295 break; | |
296 | |
297 default: | |
298 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
299 } | |
300 | |
301 ResetImage(); | |
302 | |
303 SaveDicomToMemory(target, *dicom, transferSyntax_); | |
304 } | |
305 } |